Sunday, May 18, 2014

Staking Claims

One of the most bizarre defenses of evolution, which I first encountered years ago, is that contradictory evidence doesn’t matter because it was investigated by an evolutionist. Like planting your flag on the Moon, or like a trademark or patent, the first one there, or the first one with the idea, gets to claim it for their own. Evolutionists discovered ORFans, for example, so ORFans cannot be contrary to evolution.

Another interpretation of this pretzel logic is that since the discoverer of the new evidence is still an evolutionist, that means that the evidence must not be truly contrary to evolution. It is as though the discoverer of the new evidence has some deeper understanding of the evidence, or unique ability to interpret the evidence and incorporate it into the larger body of scientific information.

This leaves us in a real bind because you can imagine what evolutionists would say if we quoted from creationists or ID scientists. Those scientists are not legitimately scientific because, unlike evolutionists, religion drives their thinking.

So for evolutionists, it’s “heads I win, tails you lose.”

If you think such obviously fallacious reasoning is restricted to the chat room hackers, think again. It is common amongst evolutionists and it was on display recently when Joel Velasco debated Paul Nelson. For instance, Nelson rightly pointed out the problems with the iconic evolutionary tree of life. Here is how Velasco responded around the [1:27:30] mark:

Yeah, I’m in that group. I was on the grant that questioned the tree of life. I presented at those conferences. I refereed papers for those journals. And I don’t know a single person in that group that denies common ancestry. So I’m really not sure what’s going on.

I was a referee on that paper. And I don’t think he’s questioning common ancestry at all. Ah, I certainly don’t and I approved the paper.

What counts is the scientific evidence, not the opinion of scientist who developed or discovered the evidence. This is not to say scientific opinion is not important. But philosophers well understand that particular findings can usually be easily assimilated into the over-arching paradigm, even if they are contradictory. Furthermore there are enormous social, career and financial pressures to conform. It means little that the person who published the evidence is still an evolutionist.

We need to examine each evidence carefully without shielding it with protectionist arguments such as “Well all the other evidence confirms evolution,” or “Well the scientist doesn’t question evolution, so the evidence can’t be a problem.”

14 comments:

CH: One of the most bizarre defenses of evolution, which I first encountered years ago, is that contradictory evidence doesn’t matter because it was investigated by an evolutionist.

This is a false dilemma.

I'd again point to the OPERA experiment. Did the contrary evidence not matter, despite not immediately falsifying c as the maximum speed in real space?

You simply have no response to this. At all. Period. Apparently, you have no criticism of it, but still reject the implications it has on how science works, in practice. That's one of the most bizarre aspects of your objections.

CH: It is as though the discoverer of the new evidence has some deeper understanding of the evidence, or unique ability to interpret the evidence and incorporate it into the larger body of scientific information.

I'd again point out, we cannot extrapolate observations without first putting them into some kind of explanatory framework. In the absence of such a framework, evidence tells us nothing one way or the other. So, if you want to label this "a deeper understanding of the evidence", so be it.

CH: So for evolutionists, it’s “heads I win, tails you lose.”

No, we tentatively adopt the model that has best withstood criticism. On the surface, it seems you reject this because, well, you object to ideas despite having no criticism of them.

Nor have you stepped up and actually explained what form this supposed "assistance" took, when it was applied, etc., despite being willing to walk you though it, step by step. Again, this is quite bizarre, don't you think?

CH: We need to examine each evidence carefully without shielding it with protectionist arguments such as “Well all the other evidence confirms evolution,” or “Well the scientist doesn’t question evolution, so the evidence can’t be a problem.”

Again, there is another response, which is illustrated in OPERA experiment.

[...] neutrinos were "observed" going faster than the speed of light. This was a serious discrepancy as well. But did this result in discarding Einstein's theory? No, it did not. A replacement theory would not only have to explain the same observations just as well, but also explain why neutrinos obeyed the speed limit in every other experiment, except OPERA.

Eventually, an explanation for the discrepancy between experiments was found: a loose cable and timer running at the wrong speed.

AFAIK, no such replacement theory exists for the discrepancy between trees WRT microRNA. "Some designer must have wanted it to appear that way" doesn't explain anything.

That's not protectionism. We looked for reasons why the observations might be wrong. This is because observations are themselves based on explanatory theories, which can also be wrong.

The fallacy in your argument is that we can simply extrapolate observations without interpreting them in some form in the first place. But, it's not out there for us to simply mechanically derive from experience.

So, the tags "Fallacies" and "False expectations" are quite appropriate for your post.

Joel Velasco here. I agree that what I said here was a poor thing to say. If I had a day to prepare a planned response to Paul's presentation, I think it would have been much better. As you will see from my explanation, part of this is clearly my fault, but if you even try at all to understand the context, it is much more clear and I think it is clearly not meant to be an argument for common ancestry, but a direct rebuttal. Go to about 1:15 in the debate. Paul said that there are lots of biologists who deny common ancestry and some of them could be debating me in his place. He put up a slide with a quote from Eugene Koonin denying the Tree of Life. I THOUGHT he had Ford Doolittle denying the Tree of Life and denying LUCA [this is my fault. He sent me his slides the night before and I saw them in the morning and saw the Ford Doolittle quotes and was angry. During the talk, I couldn't see his slides, but I was following along with the slides he sent me the night before. But he didn't actually show the Doolittle slides during the talk]. But he did show the cover of the 'Beyond the Tree of Life' issue of Biology direct saying that there is a serious debate in the biological community about common ancestry. The direct implication is that these are the articles debating common ancestry and that Koonin (and I thought Doolittle and a few others he put up) are the biologists that I could be debating. But this is just false. As I tried to explain, there is a debate about the Tree of Life - that is, whether a tree model is a good model to use for representing phylogenies. But the articles that he mentions do not deny common ancestry - the claim that we are all related. The biologists that he specifically says deny common ancestry do not deny common ancestry. How do I know this? Because I was at the conference that produced that issue, I refereed some of those papers and I am quite certain I know what it is them, and I know the authors personally and they do not deny common ancestry. This is not my own argument that common ancestry is true. This is not a question of whether the science contained in the articles is evidence against common ancestry (it isn't by the way). But that wasn't even what Paul Nelson was claiming. He was directly claiming that there was a debate in the biological community where some serious biologists were denying common ancestry and the papers that he cited as evidence for this claim are not evidence for this claim at all. The 'I am not sure what is going on here' was because frankly, I was flabbergasted and not at all sure what was going on. I would have expected Paul to know this (especially since as I said, people such as Ford Doolittle have published articles saying that he does not deny common ancestry and that is a mistaken claim that creationists have used based on quote mining - he is specifically talking about Jonathan Wells in the passage I mentioned. see Doolittle, W. F., (2009) The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them. Phil. Trans. Roy. Soc. Lond., Series B 364:2221-2228.

I agree that what I said here was a poor thing to say. If I had a day to prepare a planned response to Paul's presentation, I think it would have been much better.

Very good, fair enough. You made the argument a few times, so it did not seem to be a slip of the tongue. But you’re retracting it, so …, ah but wait a minute:

As I tried to explain, there is a debate about the Tree of Life - that is, whether a tree model is a good model to use for representing phylogenies. But the articles that he mentions do not deny common ancestry - the claim that we are all related. The biologists that he specifically says deny common ancestry do not deny common ancestry. How do I know this? Because I was at the conference that produced that issue, I refereed some of those papers and I am quite certain I know what it is them, and I know the authors personally and they do not deny common ancestry.

I think it may be a bit more nuanced than this. I don’t think you can cast the tree of life into question without calling common descent into question. I sounds like you are saying this because (i) the TOL issue is restricted to early life and/or (ii) the TOL issue is resulting in the addition of more horizontal evolution and less vertical evolution, but that doesn’t really matter because it continues to remain a story of species evolving from other species, one way or another. If I have this correct then I don’t think it is accurate to claim common descent remains unscathed.

especially since as I said, people such as Ford Doolittle have published articles saying that he does not deny common ancestry

But horizontal evolution is not common descent. It just isn’t, no matter how much lipstick you put on it.

Cornelius, I am not 'retracting' anything I said in the sense that I think something I said is false nor was anything I said 'a slip of the tongue'. What you quote in the post is exactly what I meant to say. What I am saying here is that I think I could have done better. As for 'you made the argument a few times' I am not sure what you mean by 'the argument' - the two quotes you have in this post are both from my 10 minute rebuttal period in a portion of it in which I was trying to respond to Paul's claim that there is a debate among biologists today about common ancestry. -- As for the difference between denying the tree and denying common ancestry, just read a paper about the tree of life discussion - for example, mine here: http://joelvelasco.net/Papers/VelascoTree(draftcambridge).pdf or my tree-thinking without the tree. -- I will have a paper much more on point about the relationship between the tree and common ancestry but it is under blind review right now so check my website in a few weeks. The worry about the tree is a worry that the tree is a good model of phylogeny. All humans are related. But there is a debate about whether it is appropriate to make population phylogenies of human groups or whether there was just so much interbreeding between groups that we need some kind of network (like the trellis model of Templeton). Those who say population trees are bad don't think that humans have a separate ancestry. The exact same thing applies to people who say there is so much hybridization that trees are misleading or that there is so much lateral gene transfer that trees are bad. Of course the groups that share genes horizontally ALSO share genes through common ancestry and vertical descent. If this is right, I do not understand why you would say 'i don't think it is accurate to claim common descent remains unscathed'. Maybe you have something different in mind by common descent. But I wouldn't want to build the tree picture into the very meaning of common descent. Humans share common descent. You are right, horizontal evolution itself isn't descent. Interbreeding between populations isn't common descent either. But horizontal evolution doesn't somehow undermine the fact that all life is also related by vertical common descent.

If this is right, I do not understand why you would say 'i don't think it is accurate to claim common descent remains unscathed'.

Of course scientific theories need not be perfect to be accepted. They can describe phenomena to first order, with some level of “noise” and still be considered good theories. A key question is: are the anomalies, exceptions, deviations, etc, within the reasonable noise level of the theory?

In the case of common ancestry in early evolution, there is strong evidence that the answer is “no.” That is why Woese came up with his massive horizontal evolution model. He didn’t do that for the fun of it, he did it because the data was violating common ancestry so much, and required such a massive horizontal evolution model. The data are way outside the noise level of common ancestry. Woese’s proposed horizontal evolution model is theoretical. It is a complex web of interactions and nothing like it has ever been seen in the field. It certainly is nothing like common ancestry.

Early evolution may be a safer domain in which to do justice to, and follow, the data. But there are such problems at all levels, not just early evolution. Both morphological and molecular comparisons show all kinds of deviations, way outside common ancestry’s “noise” level. So I don’t think is accurate to say “Well the tree of life may not be quite right, but common ancestry has no significant problems.”

CH: A key question is: are the anomalies, exceptions, deviations, etc, within the reasonable noise level of the theory?

And another key question is: what does falling outside this level indicate? The answer to this question will depend on your particular philosophy of science. IOW, your particular explanation for how science works, in practice. We're still waiting for you to share your explanation with us in some meaningful way.

CH: In the case of common ancestry in early evolution, there is strong evidence that the answer is “no.” That is why Woese came up with his massive horizontal evolution model. He didn’t do that for the fun of it, he did it because the data was violating common ancestry so much, and required such a massive horizontal evolution model.

First, why would Woese bother if those observations didn't matter? Isn't he an "evolutionist"?

Second, this doesn't "deviate" from the underlying explanation of conjecture, in the form of genetic variation that is random to any particular problem to solve, and criticism, in the form of natural selection. HGT is yet another form of genetic variation. And it fits with the idea that earlier cells were simpler and had an even less robust translation system that resulted in higher mutation rates that we observe in modern cells.

Third, this does not represent an ad-hoc modification to the theory because it too has necessary implications for the current state of the system, which we can test.

CH: Woese’s proposed horizontal evolution model is theoretical. It is a complex web of interactions and nothing like it has ever been seen in the field. It certainly is nothing like common ancestry.

Except, the contents of theories are tested by observations, not derived from them. This is not unique to evolutionary theory. But, by all means, feel free to explain how some other process of developing theories could work, in practice.

CH: But there are such problems at all levels, not just early evolution. Both morphological and molecular comparisons show all kinds of deviations, way outside common ancestry’s “noise” level. So I don’t think is accurate to say “Well the tree of life may not be quite right, but common ancestry has no significant problems.”

Way outside absolutely nothing but common ancestry? Yes. But outside the underlying explanation of biological Darwinism? No, it's not. Why shouldn't theories become more accurate?

Again, you're objections do not exist in a vacuum. They imply some kind of philosophy of science which you have yet to disclose.

Note: I'm not even asking you to commit to any particular view. For example, you could simply iterate over each specific philosophy of science, then point out how evolutionary theory isn't science under each specific philosophy. But this hasn't occurred either.

All theories are incomplete because they cannot take into account all parallel, yet unrelated events that could effect what we observe. It's simply not possible. IOW, you seem to be confusing scientific theories with divine prophecy, which supposedly can take into account all parallel, yet unrelated events.

Joel again. On the next point,The 'I approved of the paper' was a stupid thing to say and it reads like an appeal to (my own) authority, but again, I was flabbergasted. Paul spent time to point that the referee reports in Biology Direct were open and that he really liked that, etc. So when he put up a quote from the paper by Rob Beiko supposedly as part of an argument that ORFans are evidence against common ancestry, I was shocked and a little angry (inappropriately - in fact the Beiko quote was just part of explaining the data on orfans). Paul obviously knew I was the referee there and I felt he must be baiting me or trying to undermine me or something. Upon reflection I think it is clear he was not and it was (almost) incidental that I happened to referee that paper. And he just does like the open reviews aspect of Biology Direct and wanted to mention that. Anyway, the Beiko paper has nothing to do with common ancestry but is about trying to find computational methods which can handle huge amounts of data in a reasonably short amount of time. So at the time, it seemed to come out of the blue when I thought it had nothing to do with what we were talking about (other than 'Joel has had some interaction with him...')

Would you, on reflection, think it was worthwhile publicly debating in a video format with Paul Nelson, a well-known Creationist associated with the Discovery Institute who are not renowned as an organisation seeking scientific enlightenment.

If you think an exchange of view is worthwhile, perhaps a better method would have been a text format with plenty of time for checking references etc.

Since the days of Duane Gish, Creationists have been suspected of not being overly scrupulous in their debating tactics. Though I would concede Paul Nelson appears to have more integrity than some.

Indeed it was Nelson who famously remarked:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’-but, as yet, no general theory of biological design.

I couldn't help noticing, on checking your CV to ensure the correct honorific, that you had a position as "Ahmanson Postdoctoral Instructor in Philosophy" until last year. that wouldn't be the Howard Ahmanson, would it? :)

Alan, when I was at Caltech all I knew was that they tons of money in various 'Ahmanson funds' and there are plenty of buildings and other things named Ahmanson (like the Astronomy library). Now because of your comment, I tried to look for more information. The money comes from the Ahmanson foundation set up by Howard Ahmanson Sr. and now run by his nephews. I suspect 'the' Ahmanson you mean is Howard Jr. (his son) who has given lots of money to the discovery institute.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/